VMD-L Mailing List

From: Luca Bellarosa (lbellarosa_at_ICIQ.ES)
Date: Tue Apr 22 2014 - 10:43:46 CDT

Axel,

sorry for the late reply and thank you very much for the guide: it was very helpful!

Luca
________________________________
 Luca Bellarosa
 Postdoc Researcher, Institut Català d’Investigació Química (ICIQ)
 Av. Països Catalans 16 – 43007 Tarragona
 Tel +34 977920229 (Ext. 307) – Fax +34 977920231

 lbellarosa_at_iciq.es
________________________________

Dalla scuola di guerra della vita. Tutto ciò che non mi uccide, mi rafforza. (F.Nietzsche, "Il crepuscolo degli idoli")

________________________________________
De: Axel Kohlmeyer [akohlmey_at_gmail.com]
Enviado: miércoles, 09 de abril de 2014 17:15
Para: Luca Bellarosa
CC: vmd-l_at_ks.uiuc.edu
Asunto: Re: vmd-l: Changing colors during a dynamics

On Wed, Apr 9, 2014 at 4:29 PM, Luca Bellarosa <lbellarosa_at_iciq.es> wrote:
> Hi everybody,
>
> my name is Luca and I'm preparing the video of a dynamics (25 ps) using VMD. During this trajectory, some atoms change their coordination and I wanted to highlight this phenomenon by changing smoothly the colors of the atom. Unfortunately, I cannot manage to even change the color during a given femtosecond.
>
> My goal is the following:
> -) When the atom is 4-fold coordinated, the atom is yellow (RGB 1 1 0.36).
> -) When the atom is 5-fold coordinated, the atom is orangish (RGB 0.9 0.5 0.18).
> -) When the atom is 6-fold coordinated, the atom is red (RGB 0.8 0 0).
>
> I wrote a tcl script with the following commands:
>
> ---------------------tcl script--------------------------------------------------------------------------------
> # I read the coordination "c" from a file; "c" can be any real value between 4 and 6.
>
> set ix [expr {1.00 - ($c-4)*0.10}]
> set iy [expr {1.00 - ($c-4)*0.50}]
> set iz [expr {0.36 - ($c-4)*0.18}]
>
> color atom 262 { $ix $iy $iz } # I chose the atom 262, but it can be anything
>
> ---------------------tcl script--------------------------------------------------------------------------------
>
> But it gives me the following message: "Unable to change color name". I think I know how I can do it for all the frames, but I need to solve this problem with just one frame.
>
> Thank you in advance for any help you can give me,

have a look at chapter 5 of this (for the most part over 10 year old) tutorial:

https://sites.google.com/site/akohlmey/redirect/cpmd-vmd.pdf?attredirects=0&d=1

>
> Luca
>
>
> ________________________________
> Luca Bellarosa
> Postdoc Researcher, Institut Català d'Investigació Química (ICIQ)
> Av. Països Catalans 16 - 43007 Tarragona
> Tel +34 977920229 (Ext. 307) - Fax +34 977920231
>
> lbellarosa_at_iciq.es
> ________________________________
>
> Dalla scuola di guerra della vita. Tutto ciò che non mi uccide, mi rafforza. (F.Nietzsche, "Il crepuscolo degli idoli")
> 

--
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.